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- PDB-3d6f: Crystal structure of human caspase-1 with a naturally-occurring A... -

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Basic information

Entry
Database: PDB / ID: 3d6f
TitleCrystal structure of human caspase-1 with a naturally-occurring Arg240->Gln substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)
Components
  • (Caspase-1Caspase 1) x 2
  • N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / catalytic domain / naturally-occurring mutation / Apoptosis / Hydrolase / Protease / Thiol protease / Zymogen / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / NLRP1 inflammasome complex / icosanoid biosynthetic process / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / NLRP1 inflammasome complex / icosanoid biosynthetic process / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / caspase binding / osmosensory signaling pathway / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / Interleukin-37 signaling / pattern recognition receptor signaling pathway / cellular response to organic substance / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein autoprocessing / protein maturation / The NLRP3 inflammasome / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / positive regulation of inflammatory response / cellular response to type II interferon / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / cellular response to lipopolysaccharide / microtubule / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site ...Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide / Caspase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRosen-Wolff, A. / Roesler, J. / Romanowski, M.J.
CitationJournal: To be Published
Title: Mutated, structurally altered caspase-1 with decreased enzymatic and increased RIP2-meditated inflammatory activity leads to a new type of periodic fever (ICE fever).
Authors: Rosen-Wolff, A. / Romanowski, M.J. / Ritter, L. / Flecks, S. / Quoos, N. / Gramatt, J. / Petzold, C. / Nguyen, H.D. / Gahr, M. / Roesler, J.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3May 23, 2012Group: Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)30,8343
Polymers30,8343
Non-polymers00
Water4,432246
1
A: Caspase-1
B: Caspase-1
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide

A: Caspase-1
B: Caspase-1
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)61,6686
Polymers61,6686
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area17930 Å2
ΔGint-101 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.046, 64.046, 161.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-151-

HOH

DetailsDimer of the p20/p10 dimer

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Components

#1: Protein Caspase-1 / Caspase 1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 beta-converting enzyme / p45 / Caspase-1 subunit p20 / Caspase-1 subunit p10


Mass: 19971.967 Da / Num. of mol.: 1 / Fragment: Caspase-1 subunit p20 / Mutation: R240Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: P29466, caspase-1
#2: Protein Caspase-1 / Caspase 1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / IL-1 beta-converting enzyme / ICE / Interleukin-1 beta-converting enzyme / p45 / Caspase-1 subunit p20 / Caspase-1 subunit p10


Mass: 10389.950 Da / Num. of mol.: 1 / Fragment: Caspase-1 subunit p10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: P29466, caspase-1
#3: Protein/peptide N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Type: Peptide-like / Class: Inhibitor / Mass: 471.907 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All ...Details: Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 29, 2006
RadiationMonochromator: Asymmetric curved crystal; crystal type S(220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 27088 / % possible obs: 98.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 6.2
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.1

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sc3

1sc3


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.203 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24014 1359 5 %RANDOM
Rwork0.21421 ---
obs0.21551 25559 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.826 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2--1 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 0 246 2344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9131.9662912
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.075259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02124.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05915392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2841514
X-RAY DIFFRACTIONr_chiral_restr0.060.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1580.21047
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21477
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0820.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3742.51359
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.25252129
X-RAY DIFFRACTIONr_scbond_it1.3562.5902
X-RAY DIFFRACTIONr_scangle_it2.2075783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.966 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.345 131 -
Rwork0.268 2428 -
obs--97.97 %

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